You should not have to pay the Franchise tax in California since your LLC is registered in Colorado.
The Schedule C is part of your federal return and if you allocated all of the income from that Schedule C to Colorado as Colorado source income the Schedule C will only be in the background of your California Return. That income will be taxed by California because you are a California Resident, but you will get credit on your California return for tax paid to Colorado.
When you entered your state returns in TurboTax, did you start with Colorado and then do California? If not, I would delete your state returns and enter them in that order.
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